MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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description	Rank	Gene	Filtered	green	Value Type	Network Comparison Type	Interaction Map	red	network_comparison

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Showing element 101 to 150 of 38536 in total

Network Comparison Type  : Divided

description	Rank	Filtered	green	Value Type	Interaction Map	red	network_comparison
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	1961	1	63.0743	Rooted	High confidence	61.3419	1.02824
	2108		194.902	Ranked	Low confidence	198.65	1.01923
	2396		221.51		High confidence	220.683	1.00375
	4466		50905.5	Squared	Low confidence	49835.4	1.02147
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	921		29768.2		High confidence	25739.7	1.15651
	927		74.7636	Rooted	Low confidence	71.9022	1.0398
	993		8288.57	Measured		7982.87	1.03829
	1044		196.966	Ranked		201.723	1.02415
	1600		6788.96	Measured	High confidence	6336.22	1.07145
	2036		68.7832	Rooted		66.966	1.02714
	2366		202.529	Ranked		203.353	1.00407
	4150		44213.2	Squared	Low confidence	45383.4	1.02647
15 kda selenoprotein precursor. [swissprot;acc:o60613]	914		34456.5		High confidence	29772.1	1.15734
	1043		6933.36	Measured		6344.41	1.09283
	1334		67.2624	Rooted		64.5959	1.04128
	1948		212.432	Ranked		214.522	1.00984
	2675		43157.8	Squared	Low confidence	44774.4	1.03746
	3577		8083.96	Measured		7881.96	1.02563
	3869		73.3413	Rooted		71.3287	1.02822
	4465		201.104	Ranked		202.928	1.00907
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]	2067		8425.81	Measured		8165.8	1.03184
	2855		0.00001		High confidence	0.00001	1
				Ranked
				Squared
				Rooted
	3576		75.5218		Low confidence	73.3363	1.0298
	4126		195.778	Ranked		197.858	1.01062
	4553		44651.1	Squared		45519.8	1.01946
16.7kd protein. [refseq;acc:nm_016139]	788		45775.4			48142.9	1.05172
	3267		195.864	Ranked		198.949	1.01575
	3651		75.5801	Rooted		73.4106	1.02955
	4005		8483.17	Measured		8297.71	1.02235
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]	1051		217.998	Ranked	High confidence	211.449	1.03097
			8498.04	Measured	Low confidence	8189.31	1.0377
	1381		75.6999	Rooted		72.9975	1.03702
	1803		195.655	Ranked		199.592	1.02012
	2377		27574.1	Squared	High confidence	25809.5	1.06837
	2521		6113.96	Measured		5964.17	1.02511
	2642		63.5847	Rooted		63.9773	1.00617
	4655		45738.2	Squared	Low confidence	46495	1.01655
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829]	627	0	10050.9	Ranked		10347.7	1.02953
	631	1	8689.28	Measured		8316.12	1.04487
	768	0	39.5126	Rooted		39.0982	1.0106
	778		4869.42	Measured		4825.89	1.00902
	815		40451	Squared		40270.8	1.00447
	1116	1	76.9933	Rooted		74.1433	1.03844
	2142		192.884	Ranked		196.577	1.01915
	4933		45903.5	Squared		46142.7	1.00521
2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664]	447		45146.7			48116.9	1.06579
	3846		198.422	Ranked		201.014	1.01306

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.